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PTP database files

• PTP_Sequence_Database_Vert.xls
• PTP Sequence Database, Invertebrates and Vertebrates
• PTP_Genomic _Database_Blast_Results (Table S1).xls  
• PTP_Genomic _Database_Gene_Annotation (Table S2).xls  
• PTP_Sequence_Database_Alternative_Splicing (Table S3).xls
• Disease_Annotation_of_PTP_Loci (Table S4).xls
• Disease_Annotation_of_PTP_Loci Diabetes (Table S5).xls
• PTP_Structure_Database.xls  

PTP amino acid sequence files
Non-redundant set of human PTPs

PTP Domain D1 (37 Human Amino Acid Sequences) 

• Seq_37_ Hum PTP_Domains_D1.gp (GenPept) 
• Seq_37_ Hum PTP_Domains_D1.pir (SWISS-PROT) 
• Seq_37_ Hum PTP_Domains_D1.tfa (FASTA) 

PTP Domain D2 (12 Human Amino Acid Sequences) 

• Seq_12_ Hum PTP_Domains_D2.gp (GenPept) 
• Seq_12_ Hum PTP_Domains_D2.pir (SWISS-PROT) 
• Seq_12_ Hum PTP_Domains_D2.tfa (FASTA) 

PTP Full Length Sequences (or Longest Transcript) (37 Human Amino Acid Sequences) 

• Seq_37_ Hum_PTPs_FL.gp (GenPept) 
• Seq_37_ Hum_PTPs_FL.pir (SWISS-PROT) 
• Seq_37_ Hum_PTPs_FL.tfa (FASTA) 

Non-redundant set of vertebrate PTPs

PTP Domain D1 (135 Vertebrate Amino Acid Sequences) 

• Seq_135_Vert_PTP_Domains_D1.gp (GenPept) 
• Seq_135_Vert_PTP_Domains_D1.pir (SWISS-PROT) 
• Seq_135_Vert_PTP_Domains_D1.tfa (FASTA) 

PTP Domain D1 (Including Fragments) (170 Vertebrate Amino Acid Sequences) 

• Seq_170_Vert_PTP_Domains_D1_Incl_Fragm.gp (GenPept) 
• Seq_170_Vert_PTP_Domains_D1_Incl_Fragm.pir (SWISS-PROT) 
• Seq_170_Vert_PTP_Domains_D1_Incl_Fragm.tfa (FASTA) 

PTP Domain D2 (60 Vertebrate Amino Acid Sequences) 

• Seq_60_Vert_PTP_Domains_D2.gp (GenPept) 
• Seq_60_Vert_PTP_Domains_D2.pir (SWISS-PROT) 
• Seq_60_Vert_PTP_Domains_D2.tfa (FASTA) 

PTP Domain D2 (Including Fragments) (64 Vertebrate Amino Acid Sequences) 

• Seq_64_Vert_PTP_Domains_D2_Incl_Fragm.gp (GenPept) 
• Seq_64_Vert_PTP_Domains_D2_Incl_Fragm.pir (SWISS-PROT) 
• Seq_64_Vert_PTP_Domains_D2_Incl_Fragm.tfa (FASTA) 

PTP Domain D1 and D2 (195 Vertebrate Amino Acid Sequences) 

• Seq_195_Vert_PTP_Domains_D1_and_D2.gp (GenPept) 
• Seq_195_Vert_PTP_Domains_D1_and_D2.pir (SWISS-PROT) 
• Seq_195_Vert_PTP_Domains_D1_and_D2.tfa (FASTA)

PTP Domain D1 and D2 (Including Fragments) (234 Vertebrate Amino Acid Sequences) 

• Seq_234_Vert_PTP_Domains_D1_and_D2_Incl_Fragm.gp (GenPept) 
• Seq_234_Vert_PTP_Domains_D1_and_D2_Incl_Fragm.pir (SWISS-PROT) 
• Seq_234_Vert_PTP_Domains_D1_and_D2_Incl_Fragm.tfa (FASTA)

PTP Enzymes – All Including Partial Sequences (175 Vertebrate Amino Acid Sequences) 

• Seq_175_Vert_PTPs_ALL.gp (GenPept) 
• Seq_175_Vert_PTPs_ALL.pir (SWISS-PROT) 
• Seq_175_Vert_PTPs_ALL.tfa (FASTA) 

PTP alignment files
Non-redundant set of human PTPs

PTP Domain D1 (37 Human Sequences) 

• Alignment_37_Hum_PTP_Domains_D1.pdf
• Alignment_37_Hum_PTP_Domains_D1.xls
• Alignment_37_Hum_PTP_Domains_D1.msf (Multiple Sequence Format) 
• Alignment_37_Hum_PTP_Domains_D1.aln (Clustal) 
• Alignment_37_Hum_PTP_Domains_D1.tfa (FASTA) 
• Alignment_37_Hum_PTP_Domains_D1.apr (VectorNTI 8.0) 

PTP Domain D2 (12 Human Sequences) 

• Alignment_12_Hum_PTP_Domains_D2.pdf
• Alignment_12_Hum_PTP_Domains_D2_xls  
• Alignment_12_Hum_PTP_Domains_D2.msf (Multiple Sequence Format) 
• Alignment_12_Hum_PTP_Domains_D2.aln (Clustal) 
• Alignment_12_Hum_PTP_Domains_D2.tfa (FASTA) 
• Alignment_12_Hum_PTP_Domains_D2.apr (VectorNTI 8.0) 

PTP Domain D1 and D2 (Human Sequences) 

• Alignment_49_Hum_PTP_Domains_D1_and_D2.pdf  
• Alignment_49_Hum_PTP_Domains_D1_and_D2_xls  
• Alignment_49_hum_PTP_Domains_D1_and_D2.msf (Multiple Sequence Format) 
• Alignment_49_hum_PTP_Domains_D1_and_D2.aln (Clustal) 
• Alignment_49_hum_PTP_Domains_D1_and_D2.tfa (FASTA) 
• Alignment_49_hum_PTP_Domains_D1_and_D2.apr (VectorNTI 8.0)

Non-redundant set of vertebrate PTPs

PTP Domain D1 Alignment (135 Vertebrate Sequences) 

• Alignment_135_Vert_PTP_Domains_D1.msf (Multiple Sequence Format) 
• Alignment_135_Vert_PTP_Domains_D1.aln (Clustal) 
• Alignment_135_Vert_PTP_Domains_D1.tfa (FASTA) 
• Alignment_135_Vert_PTP_Domains_D1.apr (VectorNTI 8.0) 
• Alignment_135_Vert_PTP_Domains_D1.pdf  

PTP Domain D2 Alignment (60 Vertebrate Sequences) 

• Alignment_60_Vert_PTP_Domains_D2.msf (Multiple Sequence Format) 
• Alignment_60_Vert_PTP_Domains_D2.aln (Clustal) 
• Alignment_60_Vert_PTP_Domains_D2.tfa (FASTA) 
• Alignment_60_Vert_PTP_Domains_D2.apr (VectorNTI 8.0) 

PTP Domain D1 and D2 Alignments (195 Vertebrate Sequences) 

• Alignment_195_Vert_PTP_Domains_D1_and_D2.msf (Multiple Sequence Format) 
• Alignment_195_Vert_PTP_Domains_D1_and_D2.aln (Clustal) 
• Alignment_195_Vert_PTP_Domains_D1_and_D2.tfa (FASTA) 
• Alignment_195_Vert_PTP_Domains_D1_and_D2.apr (VectorNTI 8.0) 
• Alignment_195_Vert_PTP_Domains_D1_and_D2.pdf  

PTP Domain D1 and D2 Alignments (Including Partial Sequences) (234 Vertebrate Sequences)

• Alignment_234_Vert_PTP_Domains_D1_and_D2_All.msf (Multiple Sequence Format) 
• Alignment_234_Vert_PTP_Domains_D1_and_D2_All.aln (Clustal) 
• Alignment_234_Vert_PTP_Domains_D1_and_D2_All.tfa (FASTA) 
• Alignment_234_Vert_PTP_Domains_D1_and_D2_All.apr (VectorNTI 8.0)
• Alignment_234_Vert_PTP_Domains_D1_and_D2_All.pdf

PTP tree files

Trees are calculated from the above PTP domain sequence alignments 

• Tree_37_Hum_PTP_Domains_D1.ppt  
• Tree_37_Hum_PTP_Domains_ D1.pdf  
• Tree_37_Hum_PTP_Domains_ D1.tre (Nexus tree, bootstrapped)
• Tree_37_Hum_PTP_Domains _D1.ph (Phylip tree, bootstrapped)
• Tree_12_Hum_PTP_Domains_D2.ppt  
• Tree_12_Hum_PTP_Domains_ D2.pdf  
• Tree_12_Hum_PTP_Domains_ D2.tre (Nexus tree)
• Tree_12_Hum_PTP_Domains _D2.ph (Phylip tree)
• Tree_49_Hum_PTP_Domains_D1_and_D2.ppt  
• Tree_49_Hum_PTP_Domains_D1_and_D2.pdf  
• Tree_49_Hum_PTP_Domains_D1_and_D2.tre (Nexus tree, bootstrapped) 
• Tree_49_Hum_PTP_Domains_D1_and_D2.ph (Phylip tree, bootstrapped)
• Tree_135_Vert_PTP_Domains_D1.ppt  
• Tree_135_Vert_PTP_Domains_D1.pdf  
• Tree_135_Vert_PTP_Domains_D1.tre (Nexus tree, bootstrapped) 
• Tree_135_Vert_PTP_Domains_D1.ph (Phylip tree, bootstrapped)
• Tree_195_Vert_PTP_Domains_D1_and_D2.ppt  
• Tree_195_Vert_PTP_Domains_D1_and_D2.pdf  
• Tree_195_Vert_PTP_Domains_D1_and_D2.tre (Nexus tree, bootstrapped) 
• Tree_195_Vert_PTP_Domains_D1_and_D2.ph (Phylip tree, bootstrapped) 
• Tree_60_Vert_PTP_Domains_D2.ppt  
• Tree_60_Vert_PTP_Domains_D2.pdf  
• Tree_60_Vert_PTP_Domains_D2.tre (Nexus tree, bootstrapped) 
• Tree_60_Vert_PTP_Domains_D2.ph (Phylip tree, bootstrapped)

PTP pseudogene sequences

• Seq_12_Hum_PTP_Pseudogenes.gb (GenBank)
• Seq_12_Hum_PTP_Pseudogenes.tfa (FASTA)

• Alignment_TCPTP_Pseudogenes.pdf
• Alignment_TCPTP_Pseudogenes.msf
• Alignment_TCPTP_Pseudogenes.aln
• Alignment_TCPTP_Pseudogenes.apr

• Alignment_SHP2_Pseudogenes.pdf
• Alignment_SHP2_Pseudogenes.msf
• Alignment_SHP2_Pseudogenes.aln
• Alignment_SHP2_Pseudogenes.apr

PTP structure files

PTP X-ray crystal structures can conveniently be retrieved from the Protein Data Bank using the hyperlinked PDB entries (accession numbers) in the Excel database file: 

• PTP structure database.xls